After a disastrous event that was thought to have killed everyone outside of Tokyo, Ayato Kamina and his beloved Haruka Mishima were separated. However, three years later, their city was attacked by invaders, and Ayato met Haruka Shitow, a TERRA agent who promised to uncover the world's truth to him. This ignited a series of strange events, such as Ayato activating the RahXephon, a massive mecha, and learning that certain individuals, including his mother, had blue blood. He also discovered that he had been living in a self-contained dimension where time passed more slowly than in the outside world.